Understanding the mechanisms of soil microbial community response to climate change is critical to maintain agricultural productivity and environmental sustainability in farmland ecosystem. By combining soil transplantat experiment and PLFA (Phospholipid fatty acid) technique, this study explored the structure of microbial communities in Chao soil located at Hailun, Fengqiu and Yingtan for 6 years. The results unveiled that change of climate regimes altered some soil physicochemical properties. Soil organic matter (SOM) content was the highest in Hailun while lowest in Yingtan. The amounts of total PLFAs, Gram-positive, Gram-negative, bacterial and actinobacterial PLFAs were followed the sequence of Hailun > Fengqiu > Yingtan, and fungi to bacteria ratio was lowest in the Hailun. The PCA (Principal component analysis) showed that the structure of soil microbial communities were significantly affected by the changed climate regimes, and the samples located to the right along PC1 for Hailun and Fengqiu while left for Yingtan. The dominant PLFAs were 18:1ω7c、16:1ω5c、16:0、18:0 and 18:2ω6, 9c which were easily affected by climate regimes. Stepwise multiple regression analysis showed that annual average temperature, rainfall and SOM were the dominant factors in shaping soil microbial communities. Together, these results suggested that soil exposure to new climate regime for short time could cause a significant change of microbial community, which consequently affected biogeochemical cycles in farmland ecosystem.